Arkansas High Performace Computing Center [hpcwiki]

Infernal (“INFERence of RNA ALignment”) is for searching DNA sequence databases for RNA structure and sequence similarities. You can find more information about Infernal here.

To use Infernal the modules for its software and other dependencies need to be loaded first. The easiest way to do this is editing your .bashrc file in your $HOME directory, by adding the lines below. You may have to restart your session for this to take affect.

module load impi/5.0.0
module load gcc/4.9.1
module load infernal

Then in your $HOME directory create a directory to submit your Infernal jobs from. Copy the tutorial folder, provided by Infernal, to the directory you just made in your $HOME directory.

razor-l1:jokinsey:~$ mkdir INFERNAL-JOBS
razor-l1:jokinsey:~$ cd INFERNAL-JOBS/
razor-l1:jokinsey:~/INFERNAL-JOBS$ cp -r /share/apps/bioinformatics/infernal/infernal-1.1.1-linux-intel-gcc/tutorial .

If you see a folder named tutorial in the submission directory you created then you are ready to run the example.

In the submission directory for you Infernal jobs create a file named infernal.pbs with the information below. This is a PBS script that will be submitted to run the test job.

#!/bin/bash
#PBS -N infernal
#PBS -q tiny12core
#PBS -j oe
#PBS -o infernal.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=0:05:00

cd $PBS_O_WORKDIR
cp -r  tutorial /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

cmbuild tRNA5.cm tutorial/tRNA5.sto

cmcalibrate --forecast tRNA5.cm
cmcalibrate tRNA5.cm

cmsearch -o tRNA5.cmsearch.out tRNA5.cm tutorial/mrum-genome.fa

mkdir $PBS_O_WORKDIR/infernal.$PBS_JOBID
cp -r . $PBS_O_WORKDIR/infernal.$PBS_JOBID

This script is first running cmbuild to build a covariance model using the alignment file provided with the tutorial. Then using cmcalibrate calculates the e-values needed to search the database. Finally it searches the sequence database provided by the tutorial, and stores that output to the file tRNA5.cmsearch.out. This tutorial follows the example provided by Infernal, which you can find here.

All that's left to do is submit the job.

razor-l1:jokinsey:~/INFERNAL-JOBS$ qsub infernal.pbs

You can find the output located in the folder infernal.$PBSJOBID. If you need to review the standard output when the job was ran, it will be located in the file $PBSJOBID.OU.